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Added 'jktools' target (UCSC commandline tools)

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1 parent d50f436 commit 4426cb512a5856c719b8428be6a429e5770a03a0 @agordon committed Feb 17, 2012
Showing with 51 additions and 3 deletions.
  1. +51 −3 Makefile
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@@ -48,6 +48,40 @@ BOWTIE2=http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.0.0-beta5/bow
BOWTIE2_ZIP=$(notdir $(BOWTIE2))
BOWTIE2_DIR=$(basename $(BOWTIE2_ZIP))
+## The pre-compiled x86-x64 binaries of Jim Kent's UCSC command-line utilities
+JKTOOLS_DIR=ucsc_jktools
+JKTOOLS_URL=http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
+JKTOOLS_EXES=bedClip \
+ bedGraphToBigWig \
+ bedToBigBed \
+ bigBedInfo \
+ bigBedToBed \
+ bigBedSummary \
+ bigWigAverageOverBed \
+ bigWigInfo \
+ bigWigSummary \
+ bigWigToBedGraph \
+ bigWigToWig \
+ faToNib \
+ faToTwoBit \
+ genePredToGtf \
+ gff3ToGenePred \
+ gtfToGenePred \
+ htmlCheck \
+ hubCheck \
+ liftOver \
+ pslCDnaFilter \
+ pslPretty \
+ pslReps \
+ pslSort \
+ twoBitInfo \
+ twoBitToFa \
+ wigCorrelate \
+ wigToBigWig \
+ blat/blat \
+ blat/gfClient \
+ blat/gfServer
+
# Default URL is dummy. Use must specify a valid one
URL=foo://must/replace/this/with/real/url/of/package
@@ -250,6 +284,7 @@ all:
@echo " cufflinks"
@echo " bwa"
@echo " bedtools"
+ @echo " jktools (common UCSC command-line tools)"
@echo ""
@echo " bioinfo-install - build & install the above BioInfo packages"
@echo ""
@@ -530,13 +565,12 @@ bowtie2-install:
.PHONY: bioinfo
-bioinfo: samtools bowtie bwa bedtools tophat cufflinks
+bioinfo: samtools bowtie bwa bedtools tophat cufflinks jktools
.PHONY: bioinfo-install
-bioinfo-install: samtools_install bwa_install bowtie-install
+bioinfo-install: samtools_install bwa_install bowtie-install jktools-install bedtools-install
$(MAKE) URL="$(TOPHAT)" install-autoconf-package
$(MAKE) URL="$(CUFFLINKS)" install-autoconf-package
- $(MAKE) bedtools-install
##
@@ -609,3 +643,17 @@ bedtools:
.PHONY: bedtools-install
bedtools-install:
cp ./bedtools/bin/bedtools /usr/local/bin
+
+.PHONY: jktools
+jktools:
+ mkdir -p $(JKTOOLS_DIR)
+ ( cd $(JKTOOLS_DIR) ; \
+ for TOOL in $(JKTOOLS_EXES) ; \
+ do \
+ rm -f $${TOOL} ; \
+ wget $(JKTOOLS_URL)/$${TOOL} || exit 1; \
+ done );
+
+.PHONY: jktools-install
+jktools-install:
+ cp $(JKTOOLS_DIR)/* $(DEFAULT_INSTALLATION_PREFIX)/bin/

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